Sparsely correlated hidden Markov models with application to genome-wide location studies
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
Bellman's GAP—a language and compiler for dynamic programming in sequence analysis
Searching for virus phylotypes
Systematic inference of highways of horizontal gene transfer in prokaryotes
Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure
Fast alignment and comparison of RNA structures
APoc: large-scale identification of similar protein pockets
SIBER: systematic identification of bimodally expressed genes using RNAseq data
Grape RNA-Seq analysis pipeline environment
Reconciling differential gene expression data with molecular interaction networks
A coherent feedforward loop design principle to sustain robustness of biological networks
miRCancer: a microRNA–cancer association database constructed by text mining on literature
gKaKs: the pipeline for genome-level Ka/Ks calculation
CRAVAT: cancer-related analysis of variants toolkit
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
DSK: k -mer counting with very low memory usage
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction
Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
CePa: an R package for finding significant pathways weighted by multiple network centralities
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface
A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees